Contacts of the strand formed by residues 52 - 58 (chain H) in PDB entry 5EEZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 52 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101G TRP* 2.6 41.3 + - + +
23H GLY* 4.0 7.2 - - - -
24H LEU 3.5 3.1 - - - -
26H ARG* 3.5 1.1 + - - -
33H HIS* 2.8 19.4 + - - -
47H GLN 4.4 2.5 - - - +
48H PHE* 3.5 6.9 - - - -
49H THR* 2.9 36.8 + - - +
51H HIS* 1.3 78.5 - - - +
53H SER* 1.3 59.6 + - - +
54H ALA 3.6 20.6 - - - +
55H ILE* 3.9 19.1 - - + -
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Residues in contact with SER 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU 3.2 4.6 + - - -
25H THR 3.7 1.0 + - - -
26H ARG* 3.3 34.4 - - - +
48H PHE* 3.8 7.0 - - - -
52H THR* 1.3 75.4 - - - +
54H ALA* 1.3 59.8 + - - +
101H TRP* 3.0 31.1 + - - +
47I GLN* 3.1 33.6 + - - +
49I THR* 3.6 17.0 - - - -
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 2.9 54.3 + - + -
48H PHE* 3.8 2.0 - - - -
52H THR* 3.6 7.5 - - - +
53H SER* 1.3 79.7 + - - +
55H ILE* 1.3 62.5 + - - +
101H TRP* 4.2 14.4 - - + -
44I LEU* 4.3 5.4 - - + -
45I ILE 3.1 13.9 - - - +
46I ALA* 4.1 12.1 - - + -
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Residues in contact with ILE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G TRP* 3.9 17.3 - - + -
10H VAL* 4.0 28.7 - - + -
21H VAL* 3.7 28.3 - - + -
22H ILE 3.2 6.5 - - - +
46H ALA* 4.2 4.7 - - + +
47H GLN 4.0 13.9 - - - +
48H PHE* 3.8 19.7 - - + -
52H THR* 3.9 11.4 - - + -
54H ALA* 1.3 79.9 - - - +
56H LYS* 1.3 64.8 + - - +
57H VAL* 4.6 3.1 - - + -
44I LEU* 3.4 4.1 - - - -
45I ILE* 2.8 57.6 + - + +
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Residues in contact with LYS 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ASN 3.6 2.4 - - - +
21H VAL* 3.6 1.2 - - - -
22H ILE* 2.8 44.4 + - + +
24H LEU* 4.0 9.4 - - + +
32H PHE* 4.3 13.1 - - + -
55H ILE* 1.3 75.8 - - - +
57H VAL* 1.4 69.5 + - - +
58H ARG* 3.7 22.7 - - - +
36I GLU* 3.5 21.7 + - - +
37I LYS 3.2 23.8 + - - -
38I LEU* 3.6 15.8 - - + +
42I GLU* 3.3 25.6 + - - -
43I VAL 3.3 10.3 - - - +
44I LEU* 4.0 11.0 - - + -
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Residues in contact with VAL 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 4.1 25.1 - - + -
19H VAL* 4.1 10.3 - - + -
20H ASN 3.5 7.4 - - - +
21H VAL* 4.7 3.6 - - + -
55H ILE* 4.6 4.0 - - + -
56H LYS* 1.4 79.3 - - - +
58H ARG* 1.3 61.3 + - - +
59H GLY 4.4 0.9 - - - +
61H ALA* 4.0 15.3 - - + -
63H ILE* 4.0 21.3 - - + -
72H SER* 3.4 24.4 - - - +
42I GLU* 3.8 7.6 - - - +
43I VAL* 2.8 30.7 + - + +
45I ILE* 4.3 16.2 - - + -
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Residues in contact with ARG 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H VAL* 3.4 5.4 - - - +
20H ASN* 2.8 59.8 + - + +
22H ILE* 4.1 23.9 - - + +
32H PHE* 4.4 11.5 - - - -
56H LYS* 3.7 30.1 - - - +
57H VAL* 1.3 73.0 - - - +
59H GLY* 1.3 63.4 + - - +
42I GLU* 3.1 30.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il